Hypoxia Modulates Histone H3 Modification Patterns in Peripheral Immune Cells

Hypoxia, or reduced oxygen availability, has been shown to modulate immune cell function, contributing to the onset and pathology of diseases including cancer, sepsis, and acute and chronic lung disease. One mechanism by which hypoxia may influence immune phenotypes is through rapid modulation of gene expression via epigenetic regulation including histone modifications, DNA methylation, and RNA-mediated mechanisms. Methylation, acetylation, and phosphorylation of histones are key epigenetic regulators that allow for a rapid cellular response to environmental stressors. In this study, we investigate the specific impact of hypoxia on global histone modification patterns and expression of histone modifying enzymes responsible for these changes in peripheral immune cells. We hypothesized that if histone modifications are essential for the rapid transcriptional response to hypoxic stress, then we would observe (1) differential expression of genes associated with histone modifying enzymes, and (2) significant changes in global levels of histone modifications, including increases in modifications associated with transcriptional repression as a means of energy conservation in hypoxia. To test this hypothesis, we used both in vivo and in vitro approaches. We first performed RNA-sequencing on whole blood samples collected in 17 healthy individuals at sea level and over 3 days of acclimatization to high altitude hypoxia (3800 m elevation at Barcroft Station in the White Mountain Research Center) to examine changes in histone modifying enzyme gene expression. We also cultured primary human peripheral blood mononuclear cells (PBMCs) collected at sea level in hypoxia (1% O2) or normoxia for 24 hours. H3 histones were extracted following treatment and we quantified levels of 21 unique H3 modifications. We found that 1-3 days of acclimatization to high altitude (HA1, HA3, respectively) resulted in significant changes in expression of histone modifying enzymes within peripheral immune cells compared to sea-level values, including decreased expression of HDAC1 (HA1: log2FC = -0.29, p<0.001; HA3: log2FC = -0.46, p<0.001) and HDAC3 (HA1: log2FC = -0.34, p<0.001; HA3: log2FC = -0.48, p<0.001), and increased expression of KDM3A (HA1: log2FC = 0.28, p<0.001; HA3: log2FC = 0.12, p = 0.05) and SIRT1 (HA1: log2FC = 0.43, p<0.001; HA3: log2FC = 0.27, p<0.001), among others. Our preliminary in vitro cell culture studies also revealed that hypoxia exposure increased levels of H3K9me2 (FC = 2.55), H3K36me3 (FC = 4.74), and H3ser28P (FC = 4.21), and decreased levels of H3K4me1 (FC = 0.23), H3K4me3 (FC = 0.29), and H3K79me3 (FC = 0.75). Together, this data suggests an important role of histone modifications in regulating the rapid cellular response to hypoxia, including physiological responses during in vivo exposure. Future work will identify the precise genomic locations of these key modifications to identify epigenetic mechanisms underlying cellular and physiological responses to sustained hypoxic stress. This work was supported by a Regent's Faculty Fellowship and Regents' Faculty Development award to ECH and a White Mountain Mini Grant to KP. This abstract was presented at the American Physiology Summit 2025 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.